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-699770-254000NEW YORK CITY COLLEGE OF TECHNOLOGYThe City University Of New YorkSchool of Arts and SciencesDepartment of Biological SciencesCourse InformationCourse title:Genetics (Lecture and Laboratory)Course code:BIO2450 and BIO2450LCredit Hours:4 credit hours3 hours lecture and 3 hours lab per week for 15 weeksPrerequisite:BIO1201Text:Lecture“Concepts of Genetics, Second Edition” by Brooker RJ. ISBN: 978-0-07-352535-8LabVarious handouts will be used for all laboratories in this courseMaterialsLab coat, disposable gloves, calculatorCourse Description:This course introduces students to fundamental concepts in classical and molecular genetics. Topics are chosen to provide a broad overview of fields including Mendelian Inheritance, viral and bacterial genetics, molecular structure of genes, transcription and translation, genetic analysis, cancer genetics, and population and quantitative genetics. Laboratories complement lectures by providing a hands-on, inquiry-based approach to research questions in genetics focusing on both molecular and classical approaches.Grading Procedure (see Grading Policies for details)Lecture: 60%Lab: 40%The Lecture component will include 4 exams plus other assignments at the discretion of the instructor. The Lab component will include 4 quizzes, 5 short lab summaries, and a final full laboratory report.Course CoordinatorsDr. Christopher Blair(718) 260-5342CBlair@citytech.cuny.eduInstructorsLectureName: Dr. Christopher BlairEmail: CBlair@citytech.cuny.eduPhone: 718) 260-5342LaboratoryName: Dr. Christopher BlairEmail: CBlair@citytech.cuny.eduPhone: 718) 260-5342Grading Rubric (Combined)Students’ performance on this course will be evaluated as follows:Lecture: 60% of final grade based on 4 exams.Lab: 40% of final grade, based on quizzes, homework, and formal lab report.AssignmentsPointsNoteLaboratory GradingThere are 4 quizzes, which will account for 50% of the final lab grade.Quiz 15%Letter grades will be determined using a standard percentage point evaluation as outlined below:A: 93-100A-:90-92.9B+: 87-89.9B: 83-86.9B-:80-82.9C+: 77-79.9C70-76.9D:60-69.9F:Below 60Quiz 25%Quiz 35%Quiz 45%Homework assignments (5)worth 25% of the final lab grade10%The final laboratory report is worth 25% of the final lab grade10%Lecture gradingExam 115%Percentage Category:Exam 2 15%Lecture Exams60%Exam 315%Laboratory Quizzes20%Exam 415%Lab Homework10%Total100%Final Lab Report10%Grading Policy (Lecture) - 60% final course gradeAssignmentsPointsGradingLecture ComponentExam 125%Letter grades will be determined using a standard percentage point evaluation as outlined below:A: 93-100A-:90-92.9B+: 87-89.9B: 83-86.9B-:80-82.9C+: 77-79.9C70-76.9D:60-69.9F:Below 60Exam 225%Exam 325%Exam 425%Total100%Grading Policy (Laboratory) - 40% final course gradeAssignmentsPointsGradingLaboratory ComponentThere are 4 quizzes, which will account for 50% of the final lab grade.Quiz 112.5%Letter grades will be determined using a standard percentage point evaluation as outlined below:A: 93-100A-:90-92.9B+: 87-89.9B: 83-86.9B-:80-82.9C+: 77-79.9C70-76.9D:60-69.9F:Below 60Quiz 212.5%Quiz 312.5%Quiz 412.5%Homework assignments (5) 25%Final Laboratory Report25%Total100%Grading PolicyAll grades are counted (i.e. none are dropped). Make-ups are allowed at the discretion of the individual instructor, but are usually reserved for emergency situations or in select cases where a student has communicated with his/her instructor well ahead of time. Doctor’s notes are generally required. Approximately 5 bonus questions will be provided on each lecture exam. In addition, over the course of the semester there will be two short pop lab quizzes that will serve as extra credit. Extended Course DescriptionBIO2450 is designed to provide students with a broad introduction to the field of genetics. Today, genetics is used at least to some extent in multiple sub-disciplines within the life sciences, thus requiring a strong foundational understanding of the field. Further, with the advent of next-generation DNA sequencing technologies it has never been easier to dive into genetic analysis. The course is divided into multiple units, and topics have been carefully selected to provide a comprehensive overview of some of the more common themes as well as newer topics that are progressing at a rapid pace including bioinformatics and genomics. The first portion of the course reviews and expands upon topics covered in BIO1101 (e.g. mitosis, meiosis, recombination, etc.) and introduces students to Mendelian Inheritance. The second portion of the course discusses the molecular biology of genes and the process of DNA replication. Part IV focuses on the processes of transcription and translation. The final two units focus more on applied concepts and include biotechnology, genetic analysis and genomics, medical genetics, population genetics and quantitative genetics. Laboratories complement lectures by providing a hands-on, inquiry-based approach to research questions in genetics through utilization of both wet-lab and computational methodologies.Course Learning OutcomesBecome proficient in basic terminology used in the field of genetics.Understand Mendelian patterns of inheritance and more complex inheritance patterns.Demonstrate knowledge pertaining to viral and bacterial genetics.Acquire knowledge regarding the molecular properties of genes and chromosomes.Develop a more complete understanding of transcription, translation, and DNA replication.Become familiar with the diverse roles of genetics in the medical field.Develop a foundational understanding of evolutionary, population, and quantitative genetics.Use laboratories to develop experimental and quantitative skills.Continue to develop reading and analytical writing skills.Academic Integrity at City Tech and CUNYStudents and all others who work with information, ideas, texts, images, music, inventions, and other intellectual property owe their audience and sources accuracy and honesty in using, crediting, and citing sources. As a community of intellectual and professional workers, the College recognizes its responsibility for providing instruction in information literacy and academic integrity, offering models of good practice, and responding vigilantly and appropriately to infractions of academic integrity. Accordingly, academic dishonesty is prohibited in The City University of New York and at New York City College of Technology and is punishable by penalties, including failing grades, suspension, and expulsion.Final Laboratory ReportStudents are responsible for one full laboratory report related to EITHER the genetically modified organisms (GMO) laboratory exercise, PTC exercise, or barcoding exercise. This should be formatted as a full scientific paper with the appropriate sub-headings (Abstract, Introduction, Materials and Methods, Results, Discussion). The report should be 5-7 pages (double-spaced) exclusive of references. At least five (5) references from the primary peer-reviewed literature should be used in the report. These generally include journal articles. Websites (including Wikipedia) and popular news articles are not acceptable. The library is an excellent resource for help performing a literature search. Be careful of plagiarism and cite appropriately. Any idea that is not your own or is not common knowledge needs an appropriate citation. Reports are due on the last day of class (Week 15) and will count as 10% of the final course grade. Grading follows the rubric below.Homework (Laboratory)Throughout the semester there will be five (5) short homework assignments/summaries related to the laboratory experiments. Summaries should be approximately one page in length (single-spaced) that highlights the goals of the experiment, the methodology, results and conclusions. Tables and figures may be included. These assignments are not a full laboratory report, but short summaries of the respective exercise. Thus, you are NOT required to format the summary into specific subsections. All homework assignments are due in class one week following the relevant laboratory exercise. A grade of zero will be given for any homework assignment submitted late. Grading follows the rubric below.Grading rubric for one page summariesScoreCriteriaExcellent (5 pts)Very Good (4 pts)Good (3 pts)Fair (2 pts)Poor (1 pt)Background, scientific accuracy and relevanceProvides an excellent, yet brief background of topic and clearly states the goals and objectives of the experiment. Provides a succinct well-thought out rationale for experiment and provides accurate background information. Provides an adequate explanation of background information and purpose, but may deviate at times. Provides little background information and context. Does not demonstrate a clear understanding of purpose.Background information is missing or is inaccurate. Demonstrates lack of understanding of experimental goalsMethods and resultsAnalyses and results are clear and present with little to no errors. Reader gains important insights. All tables and figures contain informative legends and are appropriately referenced in text. Analyses and results are clear and present. Reader gains important insights, though some sections may be confusing. Tables and figures appropriate with informative legends. Analyses and results present, but are unclear. Context is provided, but may be difficult to comprehendAnalyses and results basic. Tables and/or figures lacking context and appropriate legends. Analyses and results missing. ConclusionsProvides an excellent conclusion to the summary that reiterates the primary purpose, major findings, and potential explanations for unanticipated results.Provides acceptable concluding remarks and demonstrates knowledge regarding purpose. May not include potential explanations for unexpected results. Adequate concluding remarks included. Some statements may stray from primary purpose of experiment. Few concluding remarks included that may deviate from the purpose of experiment.No conclusions are provided. Reader is confused as to purpose.Quality of writing, language and presentation Excellent spelling and grammar used throughout summary. Reader gains important insight. Summary exhibits excellent clarity that conveys meaning.Adequate spelling and grammar that conveys meaning. Reader gains important insights, though some statements may be confusing. Spelling and grammar are generally adequate and text conveys meaning, although writing is relatively basic and confusing in some places.Multiple instances of poor spelling, grammar, and sentence structure that impedes meaning. Reader gains some insight.Multiple instances of poor spelling, grammar, and sentence structure that significantly impedes meaning. Reader gains little insight.Document lengthSummary is between 1-2 pagesSummary is over 2 pages in length or summary is less than half a page. Grading rubric for final lab reportScoreCriteriaExcellent (5 pts)Very Good (4 pts)Good (3 pts)Fair (2 pts)Poor (1 pt)Appropriate sectionsAll sections of report presentOne section of report missing. Two sections of report missing.Three sections of report missing. Four or more sections of report missing. Introduction, scientific accuracy and relevanceProvides an excellent introduction of topic and clearly states the goals and objectives of the experiment. Provides adequate citations.Provides a succinct well-thought out rationale for experiment and provides accurate background information. Provides an adequate explanation of background information and purpose, but may deviate at times. Few statements contain citations.Provides little background information and context. Does not demonstrate a clear understanding of purpose. Citations generally lacking.Introduction section is inaccurate or missing. Demonstrates lack of understanding of experimental goals. Citations generally lacking.Methods and resultsAnalyses and results are clear and present with little to no errors. Reader gains important insights. All tables and figures contain informative legends and are appropriately referenced in text. Analyses and results are clear and present. Reader gains important insights, though some sections may be confusing. Tables and figures appropriate with informative legends. Analyses and results present, but are unclear. Context is provided, but may be difficult to comprehendAnalyses and results basic. Tables and/or figures lacking context and appropriate legends. Analyses and results missing. Discussion and conclusionsProvides an excellent discussion of results in light of other recent peer-reviewed research. Does not simply restate results. Cites appropriately.Discussion is present and reasonably well developed. Most statements contain appropriate citations, but organization could be improved. Discussion is present, but basic. Some statements may stray from primary purpose of experiment. Citations are infrequently used.Limited Discussion that may deviate from the purpose of experiment. Citations are extremely limited.Discussion is missing or ambiguous. Reader is confused as to purpose. Citations are missing. Quality of writing, language and presentation Excellent spelling and grammar used throughout report. Reader gains important insight. Report exhibits excellent clarity that conveys meaning.Adequate spelling and grammar that conveys meaning. Reader gains important insights, though some statements may be confusing. Spelling and grammar are generally adequate and text conveys meaning, although writing is relatively basic and confusing in some places.Multiple instances of poor spelling, grammar, and sentence structure that impedes meaning. Reader gains some insight.Multiple instances of poor spelling, grammar, and sentence structure that significantly impedes meaning. Reader gains little insight.References>5 references from peer-reviewed literature. Reference section present with no formatting errors.>5 references from peer-reviewed literature. Reference section present with few formatting errors.<5 references from peer-reviewed literature. Reference section present with no formatting errors.<5 references from peer-reviewed literature. Reference section present with few formatting errors.<5 references from peer-reviewed literature. Reference section missing or contains numerous errors.Document lengthLab report between 5-7 pagesLab report <5 or >7 pages Library Support for Undergraduate ResearchStudent Services: Student Services page on the Library’s website features links to:Ask Us (24/7 online chat reference service)borrowing/renewing informationlibrary technology informationcitations and writing guideinterlibrary loan informationhow to reserve group study roomsIt’s Your Library! student information handout ()Ask a Librarian: web chat with a librarianStudents can also: call the Library during open hours, email us, or make a one-on-one research appointment (or stop by the Ask a Librarian desk when the Library is open)Research Guides by Subject: to research using books, articles, database, internet, and other sources for selected disciplines and departments at City TechContact your library faculty subject specialist to request a research guide for your discipline: and Formatting Guides: The Library’s research guide for citation styles, formatting, and writing research papers.Includes suggested citation and research management tools: : , slideshow, and text-based tutorials on the research process, evaluating information, using library and internet resources, and other research topicsThe Library has an instructional design intern working with us this year to help revise these tutorials and create new tutorials, let us know if there are specific kinds of tutorials that would be useful for your studentsLecture ScheduleChapters are indicated for the 2nd Edition of “Concepts of Genetics” by R. Brooker McGraw Hill PublishersUnit 1 – Patterns of InheritanceWeek 1Overview of GeneticsGene expressionGenotype & phenotypeThe study of geneticsReproduction and Chromosome TransmissionChromosomal featuresMitosis & meiosisSexual reproductionCh. 1Pg. 1 – 19Ch. 2Pg. 20 - 41Week 2Mendelian InheritanceGregor Mendel and his pea plantsLaws of Segregation and Independent AssortmentInheritance patterns and probabilityCh. 3Pg. 42 - 72Week 3 Sex Determination and Sex ChromosomesGenetics of sex determination Dosage compensation & X-chromosome inactivationSex chromosome properties and transmission patternsExtensions of Mendelian InheritanceDominant vs. recessive allelesGene expression and the environmentDominance and allele interactionsSex-influenced inheritancePleiotropy, epistasis and gene interactionsExtranuclear InheritanceChloroplast DNAMitochondrial DNATheory of endosymbiosisCh. 4Pg. 73 – 89Ch. 5Pg. 90 – 112Ch. 6Pg. 113-120Week 4EXAM 1 (Background, mitosis, meiosis, Mendelian genetics, sex determination, extranuclear inheritance)Genetics of BacteriaOverview of bacterial reproductionConjugation, transduction, and transformationEvolution of antibiotic resistanceGenetics of VirusesStructure of virusesViral reproductionCh. 9Pg. 184 – 205Ch. 10Pg. 206 - 219Unit II - Molecular Structure and Genetic ReplicationWeek 5Molecular Structure of DNA and RNADNA and geneticsMolecular structure of nucleotides Discovery and structure of the DNA double helixMolecular structure of RNACh. 11Pg. 220 - 241Week 6Molecular Structure and Organization of ChromosomesOrganization and structure of bacterial chromosomesEukaryotic genome sizesOrganization and structure of eukaryotic chromosomes in dividing and non-dividing cellsCh. 12Pg. 242 - 261Week 7DNA ReplicationOverview of DNA replicationBacterial DNA replication – replication forksBacterial DNA replication – synthesisBacterial DNA replication – accuracyEukaryotic DNA replicationCh. 13Pg. 262 - 285Unit III – Molecular Properties of GenesWeek 8EXAM 2 (Bacterial and viral genetics, molecular structure of DNA, RNA, chromosomes, DNA replication)Gene Transcription and RNA ModificationOverview of transcriptionTranscription in BacteriaTranscription in EukaryaRNA editingCh. 14Pg. 286 - 312Week 9Translation of mRNAGenes and proteinsThe genetic code and protein synthesisStructure and function of tRNAsStructure and function of ribosomesStages of translationCh. 15Pg. 313 - 342Unit IV: Genetic TechnologiesWeek 10BiotechnologyMicroorganisms and biotechnologyGenetically modified animalsStem cells and cloningGenetically modified plantsHuman disease and gene therapyCh. 21Pg. 477 - 501Unit IV: Genetic TechnologiesWeek 11EXAM 3 (Gene transcription, translation, and biotechnology) Genomics I: Analysis of DNAOverview of chromosome mappingCytogenetic mappingLinkage mappingPhysical mappingGenome sequencingMetagenomicsCh. 22Pg. 502 - 527Week 12Genomics II: Functional Genomics, Proteomics, and BioinformaticsFunctional genomicsProteomicsBioinformaticsCh. 23Pg. 528 - 548Unit V: Genetic Analysis of Individuals and PopulationsWeek 13Medical Genetics and CancerInheritance of genetic diseasesGenetic screening and detection of disease-causing allelesPrions and diseaseGenetics and cancerPersonalized medicineCh. 24Pg. 549 - 582Week 14Population GeneticsHardy-Weinberg equilibriumNatural selectionGenetic driftMigrationNonrandom matingMutation as the ultimate source of genetic variationCh. 25Pg. 583 - 612Week 15Quantitative GeneticsOverview of quantitative geneticsStatistical methodsPolygenic inheritanceHeritabilityArtificial selection and selective breedingCh. 26Pg. 613 - 638EXAM 4 - FINAL (Genomics I, Genomics II, Medical Genetics, Population Genetics, Quantitative Genetics)Laboratory ScheduleHandouts will be used for all laboratories in this course. These will be posted to OpenLab site () and must be printed out and brought to class.Week 1Introduction to GeneticsProbability, Mendelian Genetics, chi-square and measurements,DateWeek 2Cytogenetics and KaryotypingChromosomal alterations and human diseaseDateWeek 3Mitosis & MeiosisSordaria recombination and genetic crossesHomework 1: Cytogenetics write-up dueDateWeek 4Quiz 1 – Introduction, Cytogenetics, Mitosis, MeiosisMonohybrid and Dihybrid CrossesFruit fly (Drosphila) genetics Lab 1Population GeneticsHuman blood type frequencies Lab 1Homework 2: Sordaria write-up dueDateWeek 5Monohybrid and Dihybrid CrossesFruit fly (Drosphila) genetics Lab 2Population GeneticsHuman blood type frequencies Lab 2DateWeek 6Monohybrid and Dihybrid CrossesFruit fly (Drosphila) genetics Lab 3Simulating Population Genetic ProcessesGenetic drift, mutation, gene flow, natural selectionDateWeek 7Monohybrid and Dihybrid CrossesFruit fly (Drosphila) genetics Lab 4Lab Review (Crosses and Population Genetics)DateWeek 8Quiz 2 – Inheritance and Population GeneticsDNA profiling in forensic sciencePipetting and DNA fingerprinting Lab 1 (restriction digests)Homework 3: Genetic crosses write-up dueHomework 4: Blood typing and population genetics write-up dueDateWeek 9DNA profiling in forensic scienceDNA fingerprinting Lab 2 (gel electrophoresis and analysis)DateWeek 10Quiz 3 – DNA FingerprintingMolecular Genetics, PCR, and GenotypingPTC genetics and GMO Lab 1 (DNA extraction and PCR)Homework 5: DNA fingerprinting write-up dueDateWeek 11Molecular Genetics, PCR, and GenotypingPTC genetics and GMO Lab 2 (restriction enzyme digestion and gel electrophoresis)DateWeek 12Molecular Genetics, PCR, and GenotypingPTC genetics and GMO Lab 3 (lecture, data analysis, and review questions)DateWeek 13DNA Barcoding and Evolutionary GeneticsDNA extraction and PCR from fish samplesDateWeek 14DNA Barcoding and Evolutionary GeneticsGel electrophoresis, BLAST, multiple sequence alignment and phylogenetic inferenceDateWeek 15Quiz 4 – Molecular and Evolutionary GeneticsDateFull Laboratory Report Due (PTC, GMO OR Barcoding) ................
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